Re: [Freesurfer] Average brain error

[Anna Rotarska-Jagiela]

Dear Doug,
thank you for your response. The path you named is added. Is there anything
else we can check?
Anna

2009/11/16 Douglas N Greve 

> Try adding $FREESURFER_HOME/fsfast/bin to your path.
>
>
> doug
>
> Anna Rotarska-Jagiela wrote:
> >
> >
> > Dear Freesurfer Users,
> > during the creation of average brain with Freesurfer, I got the
> > following ERROR message:
> > > > getpwdcmd: command not found
> > > > ERROR: format for rh.orig.avg.area.mgh not recognized.
> > > > ERROR: make_average_surface
> >
> > do you have any idea what this might be? The Freesurfer version I'm
> > using is 4.4.0. I also attach the log file.
> > I would appreciate your help.
> > Sincerely,
> > Anna Rotarska-Jagiela
> >
> >
> >
> > --
> > --
> > Dr. Anna Rotarska-Jagiela
> > Max Planck Institute for Brain Research
> > Department of Neurophysiology
> > Deutschordenstr. 46
> > 60528 Frankfurt a.M.
> > Germany
> > Email: rotar...@mpih-frankfurt.mpg.de
> > 
> > Phone: +49 69 6301 83782
> > Fax: +49 69 6301 3833
> > --
> > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
> > --
> > 
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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>



-- 
--
Dr. Anna Rotarska-Jagiela
Max Planck Institute for Brain Research
Department of Neurophysiology
Deutschordenstr. 46
60528 Frankfurt a.M.
Germany
Email: rotar...@mpih-frankfurt.mpg.de
Phone: +49 69 6301 83782
Fax: +49 69 6301 3833
--
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
--
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[Freesurfer] reply

[Jared Price]

Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz 
--regheader -o ...This created a volume but the same issue 
remained.  When I load a segmentation on top of the created volume, 
tkmedit won't let me alter the segmentation.  If I use "new 
segmentation" as opposed to loading a previous segmentation (e.g. the 
aseg.mgz volume) then the segmentation works fine.  Anyway, what I would 
like to do is put a volume as similar to the original dicoms as possible 
upon which a manual segmentation can be performed in tkmedit.  Any other 
thoughts?
Jared

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[Freesurfer] follow-up

[Jared Price]

...Also, I should mention that slice thickness in the MRI acquisition 
sequence was 1.3 mm so the native voxels are not 1x1x1.

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Re: [Freesurfer] edits to pial surface

[Bruce Fischl]

Hi Dana,

what's the bright stuff out near the pial surface? Is it dura? It's hard 
to tell from just a single slice. If it is, then you could try erasing 
it. Looks like there were also segmentation/topology fixing errors in the 
right superior temporal gyrus, which you could fix. Finally, you can try 
putting some control points near the base of some off the wm strands in the 
left temporal white matter.

cheers
Bruce


On Tue, 17 Nov 2009, Dana W. Moore wrote:

> Hi everyone,
>
> I have an image in which the pial surface left out portions of the cortex 
> (see left temporal lobe below).  I am not sure how to go about editing this. 
> I tried adding control points to the brainmask.mgz volume and running 
> -autorecon2-cp -autorecon3, but the result seems unchanged (see control 
> points in picture below).  Did I do something wrong?  The edit voxels tool I 
> believe would help if the problem was that these voxels had been removed 
> during skull-stripping, but this is not the case--they were just excluded 
> from the pial boundary.
>
> Thanks,
> Dana
>
> Emacs!
>
>
>
> Dana W. Moore, Ph.D.
> Neuropsychology Fellow
> Cornell Neuropsychology Service
> Weill Medical College of Cornell University
> New York Presbyterian Hospital
> Department of Neurology & Neuroscience
> 428 East 72nd Street, Suite 500
> New York, NY 10021
> Phone: 212-746-2823
> Fax: 212-746-5584
> Email: dwm2...@med.cornell.edu
>
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[Freesurfer] extract aparc.anot area

[simon]

Hi everyone,

 

I need to draw Heschl gyri on freesurfer pial surface of my subjects but
it’s not easy because this area is not directly visible. So:

1. Is there a simple mean to cut the surface to see more internal areas with
freesurfer tools (or other???) ?

2. Is it possible to extract only desired areas from the
“aparc.annot.a2005s” files and how to modify them manually? 

 

Thanks

 

 

Grégory SIMON

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[Freesurfer] FreeSurferColorLUT for FSL

[Nasim Maleki]

Dear all,

I would like to view the aparc.a2009s+aseg files in FSL and therefore  
I need to make LUTs for FSL from the FreeSurferColorLUT. I was just  
curious to know if any of you has ever done this and if there is an  
easy way around it.

Thanks for your help in advance,
Nasim 
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[Freesurfer] moving 001.mgz to anatomical space

[Jared Price]

 I see the mistake I made.  Works well now.  Thanks for the help.
Jared

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Re: [Freesurfer] extract aparc.anot area

[Christophe Destrieux]

Hi Grégory

In the 2005 version of the sulco-gyral based atlas, you should find a 
label called "transverse temporal gyrus" that correspond to the most 
anterior one that is supposed to correspond to primary auditory cortex ; 
when posterior one(s) was(ere) present it(they) was(were) included into 
the planum temporale label

We had several talks on the list with Narly Golestani ; you should find 
info's in :

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11835.html

cheers
>
> Hi everyone,
>
> I need to draw Heschl gyri on freesurfer pial surface of my subjects 
> but it’s not easy because this area is not directly visible. So:
>
> 1. Is there a simple mean to cut the surface to see more internal 
> areas with freesurfer tools (or other???) ?
>
> 2. Is it possible to extract only desired areas from the 
> “aparc.annot.a2005s” files and how to modify them manually?
>
> Thanks
>
> Grégory SIMON
>
> 
>
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-- 
Christophe Destrieux
Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - France
tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07



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[Freesurfer] ICV for incomplete whole brain coverage

[Juranek, Jenifer]

A colleague asked me to look at some T1s for possible Freesurfer analyses. 
Unfortunately, several subjects do not have whole brain acquisitions (I know, 
quite unexpected and disappointing). Would it be possible to correct volumes of 
subcortical structures (which are covered by the acquisition) for ICV in the 
absence of whole brain coverage? The T1s were acquired in the coronal 
plane...so typically brain tissue is missing in either the anterior and/or 
posterior regions.

I reflexively think that whole brain coverage is required for accurate ICV 
calculated by Freesurfer...but I'm not positive.

Many Thanks for any thoughts you might have,
Jenifer


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Re: [Freesurfer] ICV for incomplete whole brain coverage

[Bruce Fischl]

Hi Jenifer,

how much is missing? If a substantial amount I would think things would 
fail, including the segmentation itself, but we very rarely do this.

Bruce

On Tue, 17 Nov 2009, Juranek, Jenifer wrote:

> A colleague asked me to look at some T1s for possible Freesurfer analyses. 
> Unfortunately, several subjects do not have whole brain acquisitions (I know, 
> quite unexpected and disappointing). Would it be possible to correct volumes 
> of subcortical structures (which are covered by the acquisition) for ICV in 
> the absence of whole brain coverage? The T1s were acquired in the coronal 
> plane...so typically brain tissue is missing in either the anterior and/or 
> posterior regions.
>
> I reflexively think that whole brain coverage is required for accurate ICV 
> calculated by Freesurfer...but I'm not positive.
>
> Many Thanks for any thoughts you might have,
> Jenifer
>
>
>
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[Freesurfer] tkmedit

[Rajagopalan, Venkateswaran]

Hello,

I am new to freesurfer, i having the following problem. I placed my subject's 
data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit sub1 vol1 -f 
$bme/home..Desktop/test" the following command to open and view my image and i 
get the following error " bme undefined variable. What is the mistake i am 
doing here. How can i access the folders created in Desktop since i don't have 
privileges to create or access folders in Freesurfer directory as my freesurfer 
runs from the server.

Thanks

venkateswaran 

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Re: [Freesurfer] Average brain error

[Douglas N Greve]

What happens when you type

which getpwdcmd

And can you see the file in $FREESURFER_HOME/fsfast/bin?

Anna Rotarska-Jagiela wrote:
> Dear Doug,
> thank you for your response. The path you named is added. Is there 
> anything else we can check?
> Anna
>
> 2009/11/16 Douglas N Greve  >
>
> Try adding $FREESURFER_HOME/fsfast/bin to your path.
>
>
> doug
>
> Anna Rotarska-Jagiela wrote:
> >
> >
> > Dear Freesurfer Users,
> > during the creation of average brain with Freesurfer, I got the
> > following ERROR message:
> > > > getpwdcmd: command not found
> > > > ERROR: format for rh.orig.avg.area.mgh not recognized.
> > > > ERROR: make_average_surface
> >
> > do you have any idea what this might be? The Freesurfer version I'm
> > using is 4.4.0. I also attach the log file.
> > I would appreciate your help.
> > Sincerely,
> > Anna Rotarska-Jagiela
> >
> >
> >
> > --
> > --
> > Dr. Anna Rotarska-Jagiela
> > Max Planck Institute for Brain Research
> > Department of Neurophysiology
> > Deutschordenstr. 46
> > 60528 Frankfurt a.M.
> > Germany
> > Email: rotar...@mpih-frankfurt.mpg.de
> 
> >  >
> > Phone: +49 69 6301 83782
> > Fax: +49 69 6301 3833
> > --
> > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
> > --
> >
> 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> -- 
> --
> Dr. Anna Rotarska-Jagiela
> Max Planck Institute for Brain Research
> Department of Neurophysiology
> Deutschordenstr. 46
> 60528 Frankfurt a.M.
> Germany
> Email: rotar...@mpih-frankfurt.mpg.de 
> 
> Phone: +49 69 6301 83782
> Fax: +49 69 6301 3833
> --
> http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
> --

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] Clusterwise Correction for Multiple Comparisons error

[Weisinger, Brian (NIH/OD) [E]]

I am trying to do the clusterwise correction for multiple comparisons and came 
upon a problem that maybe someone can help me with.

 ri_volcluster --in brianweisinger/g1g2.intercept/sig.mgh --csd 
brianweisinger/csd/mc-z.negative.j001-g1g2.intercept.csd --mask 
brianweisinger/mask.mgh --cwsig 
brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.mgh --vwsig 
brianweisinger/g1g2.intercept/mc-z.negative.sig.voxel.mgh --sum 
brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.summary --ocn 
brianweisinger/g1g2.intercept/mc-z.negative.sig.ocn.mgh --csdpdf 
brianweisinger/g1g2.intercept/mc-z.negative.pdf.dat
Adjusting threshold for 1-tailed test.
 If the input is not a -log10(p) volume, re-run with --no-adjust.
INFO: loading mask volume: brianweisinger/mask.mgh
INFO: MRIbinarize01(): nhits = 118078
 Found 118078 voxels in mask
 Search Space = 118078 mm3
Computing voxel-wise significance
 CSDpvalMaxSigMap(): found 0/118078 above 0
ERROR: initializing hit map

It made some of the CSD files but not all of them. Any ideas?

 Thank you for your help.

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Re: [Freesurfer] reply

[Douglas N Greve]

Sorry, add --inv to the cmd line

Jared Price wrote:
> Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz 
> --regheader -o ...This created a volume but the same issue 
> remained.  When I load a segmentation on top of the created volume, 
> tkmedit won't let me alter the segmentation.  If I use "new 
> segmentation" as opposed to loading a previous segmentation (e.g. the 
> aseg.mgz volume) then the segmentation works fine.  Anyway, what I would 
> like to do is put a volume as similar to the original dicoms as possible 
> upon which a manual segmentation can be performed in tkmedit.  Any other 
> thoughts?
> Jared
>
> ___
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>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] FreeSurferColorLUT for FSL

[Douglas N Greve]

Sorry, I have not. Let us know if you get it to work.

doug

Nasim Maleki wrote:
> Dear all,
>
> I would like to view the aparc.a2009s+aseg files in FSL and therefore  
> I need to make LUTs for FSL from the FreeSurferColorLUT. I was just  
> curious to know if any of you has ever done this and if there is an  
> easy way around it.
>
> Thanks for your help in advance,
> Nasim 
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>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] tkmedit

[Douglas N Greve]

You should not use the -f option with the subject/volume option. Try 
using -aux instead.

Rajagopalan, Venkateswaran wrote:
>
> Hello,
>
> I am new to freesurfer, i having the following problem. I placed my 
> subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit 
> sub1 vol1 -f $bme/home..Desktop/test" the following command to open 
> and view my image and i get the following error " bme undefined 
> variable. What is the mistake i am doing here. How can i access the 
> folders created in Desktop since i don't have privileges to create or 
> access folders in Freesurfer directory as my freesurfer runs from the 
> server.
>
> Thanks
>
> venkateswaran
>
> ===
>
> P Please consider the environment before printing this e-mail
>
>
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2009).  
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>   
> 
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Clusterwise Correction for Multiple Comparisons error

[Douglas N Greve]

Looks like it did not find any vertices above the threshold that you 
used for the simulation (though it should give a better error msg). 
Before you run the simulation, you can look at the map at your given 
threshold. If there are no vertices above threshold, then nothing is 
going to show up in the simulation.

doug

Weisinger, Brian (NIH/OD) [E] wrote:
> I am trying to do the clusterwise correction for multiple comparisons and 
> came upon a problem that maybe someone can help me with.
>
>  ri_volcluster --in brianweisinger/g1g2.intercept/sig.mgh --csd 
> brianweisinger/csd/mc-z.negative.j001-g1g2.intercept.csd --mask 
> brianweisinger/mask.mgh --cwsig 
> brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.mgh --vwsig 
> brianweisinger/g1g2.intercept/mc-z.negative.sig.voxel.mgh --sum 
> brianweisinger/g1g2.intercept/mc-z.negative.sig.cluster.summary --ocn 
> brianweisinger/g1g2.intercept/mc-z.negative.sig.ocn.mgh --csdpdf 
> brianweisinger/g1g2.intercept/mc-z.negative.pdf.dat
> Adjusting threshold for 1-tailed test.
>  If the input is not a -log10(p) volume, re-run with --no-adjust.
> INFO: loading mask volume: brianweisinger/mask.mgh
> INFO: MRIbinarize01(): nhits = 118078
>  Found 118078 voxels in mask
>  Search Space = 118078 mm3
> Computing voxel-wise significance
>  CSDpvalMaxSigMap(): found 0/118078 above 0
> ERROR: initializing hit map
>
> It made some of the CSD files but not all of them. Any ideas?
>
>  Thank you for your help.
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] tkmedit

[Bruce Fischl]

but the volume needs to be in the subjects's mri dir. Alternatively, you 
can use -f to path to it directly. That is:

tkmedit f- Desktop/test/sub1/vol1.mgz

cheers,
Bruce
On Tue, 17 Nov 2009, Douglas N 
Greve wrote:

> You should not use the -f option with the subject/volume option. Try
> using -aux instead.
>
> Rajagopalan, Venkateswaran wrote:
>>
>> Hello,
>>
>> I am new to freesurfer, i having the following problem. I placed my
>> subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit
>> sub1 vol1 -f $bme/home..Desktop/test" the following command to open
>> and view my image and i get the following error " bme undefined
>> variable. What is the mistake i am doing here. How can i access the
>> folders created in Desktop since i don't have privileges to create or
>> access folders in Freesurfer directory as my freesurfer runs from the
>> server.
>>
>> Thanks
>>
>> venkateswaran
>>
>> ===
>>
>> P Please consider the environment before printing this e-mail
>>
>>
>>
>> Cleveland Clinic is ranked one of the top hospitals
>> in America by U.S.News & World Report (2009).
>> Visit us online at http://www.clevelandclinic.org for
>> a complete listing of our services, staff and
>> locations.
>>
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>> Confidentiality Note:  This message is intended for use
>> only by the individual or entity to which it is addressed
>> and may contain information that is privileged,
>> confidential, and exempt from disclosure under applicable
>> law.  If the reader of this message is not the intended
>> recipient or the employee or agent responsible for
>> delivering the message to the intended recipient, you are
>> hereby notified that any dissemination, distribution or
>> copying of this communication is strictly prohibited.  If
>> you have received this communication in error,  please
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Re: [Freesurfer] Average brain error

[Anna Rotarska-Jagiela]

When I type which getpwdcmd, I get:
/apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd
And I checked, the file is there.

Anna


2009/11/17 Douglas N Greve 

> What happens when you type
>
> which getpwdcmd
>
> And can you see the file in $FREESURFER_HOME/fsfast/bin?
>
> Anna Rotarska-Jagiela wrote:
>
>> Dear Doug,
>> thank you for your response. The path you named is added. Is there
>> anything else we can check?
>> Anna
>>
>> 2009/11/16 Douglas N Greve > gr...@nmr.mgh.harvard.edu>>
>>
>>
>>Try adding $FREESURFER_HOME/fsfast/bin to your path.
>>
>>
>>doug
>>
>>Anna Rotarska-Jagiela wrote:
>>>
>>>
>>> Dear Freesurfer Users,
>>> during the creation of average brain with Freesurfer, I got the
>>> following ERROR message:
>>> > > getpwdcmd: command not found
>>> > > ERROR: format for rh.orig.avg.area.mgh not recognized.
>>> > > ERROR: make_average_surface
>>>
>>> do you have any idea what this might be? The Freesurfer version I'm
>>> using is 4.4.0. I also attach the log file.
>>> I would appreciate your help.
>>> Sincerely,
>>> Anna Rotarska-Jagiela
>>>
>>>
>>>
>>> --
>>> --
>>> Dr. Anna Rotarska-Jagiela
>>> Max Planck Institute for Brain Research
>>> Department of Neurophysiology
>>> Deutschordenstr. 46
>>> 60528 Frankfurt a.M.
>>> Germany
>>> Email: rotar...@mpih-frankfurt.mpg.de
>>
>>> >>
>>> Phone: +49 69 6301 83782
>>> Fax: +49 69 6301 3833
>>> --
>>> http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
>>> --
>>>
>>
>>  
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>
>>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>--
>>Douglas N. Greve, Ph.D.
>>MGH-NMR Center
>>gr...@nmr.mgh.harvard.edu 
>>
>>Phone Number: 617-724-2358
>>Fax: 617-726-7422
>>
>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>>FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>___
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>>
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> --
>> --
>> Dr. Anna Rotarska-Jagiela
>> Max Planck Institute for Brain Research
>> Department of Neurophysiology
>> Deutschordenstr. 46
>> 60528 Frankfurt a.M.
>> Germany
>> Email: rotar...@mpih-frankfurt.mpg.de > rotar...@mpih-frankfurt.mpg.de>
>>
>> Phone: +49 69 6301 83782
>> Fax: +49 69 6301 3833
>> --
>> http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
>> --
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>


-- 
--
Dr. Anna Rotarska-Jagiela
Max Planck Institute for Brain Research
Department of Neurophysiology
Deutschordenstr. 46
60528 Frankfurt a.M.
Germany
Email: rotar...@mpih-frankfurt.mpg.de
Phone: +49 69 6301 83782
Fax: +49 69 6301 3833
--
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
--
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Re: [Freesurfer] Average brain error

[Douglas N Greve]

And does the "getpwdcmd: command not found" still occur?

Anna Rotarska-Jagiela wrote:
> When I type which getpwdcmd, I get: 
> /apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd
> And I checked, the file is there.
>
> Anna
>
>
> 2009/11/17 Douglas N Greve  >
>
> What happens when you type
>
> which getpwdcmd
>
> And can you see the file in $FREESURFER_HOME/fsfast/bin?
>
> Anna Rotarska-Jagiela wrote:
>
> Dear Doug,
> thank you for your response. The path you named is added. Is
> there anything else we can check?
> Anna
>
> 2009/11/16 Douglas N Greve  
>  >>
>
>
>Try adding $FREESURFER_HOME/fsfast/bin to your path.
>
>
>doug
>
>Anna Rotarska-Jagiela wrote:
>>
>>
>> Dear Freesurfer Users,
>> during the creation of average brain with Freesurfer, I
> got the
>> following ERROR message:
>> > > getpwdcmd: command not found
>> > > ERROR: format for rh.orig.avg.area.mgh not recognized.
>> > > ERROR: make_average_surface
>>
>> do you have any idea what this might be? The Freesurfer
> version I'm
>> using is 4.4.0. I also attach the log file.
>> I would appreciate your help.
>> Sincerely,
>> Anna Rotarska-Jagiela
>>
>>
>>
>> --
>> --
>> Dr. Anna Rotarska-Jagiela
>> Max Planck Institute for Brain Research
>> Department of Neurophysiology
>> Deutschordenstr. 46
>> 60528 Frankfurt a.M.
>> Germany
>> Email: rotar...@mpih-frankfurt.mpg.de
> 
> >
>>  
> >>
>> Phone: +49 69 6301 83782
>> Fax: +49 69 6301 3833
>> --
>> http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
>> --
>>
>  
>  
> 
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
> 
> >
>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
> 
>  >
>
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
>
>
>FileDrop:
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> -- 
> --
> Dr. Anna Rotarska-Jagiela
> Max Planck Institute for Brain Research
> Department of Neurophysiology
> Deutschordenstr. 46
> 60528 Frankfurt a.M.
> Germany
> Email: rotar...@mpih-frankfurt.mpg.de
> 
>  >
>
> Phone: +49 69 6301 83782
> Fax: +49 69 6301 3833
> --
> http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
> --
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportin

[Freesurfer] Best way to convert Philips par/rec to mgz

[Julie McEntee]

Hello,

I have T1-weighted data from Philips 3 T scanner obtained at a resolution of
0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size =
int16) format. I would like to preserve the acquisition resolution of the
data in par/rec format; what is the best way to convert such data to mgz
format for analysis in freesurfer? A command line example would be helpful,
as I am new to freesurfer.

Thanks for your help,

Julie

Julie E. McEntee, MA, CCRP
Senior Research Program Coordinator
Department of Psychiatry- Neuroimaging
Johns Hopkins University School of Medicine
600 N. Wolfe St./Phipps 300
Baltimore, MD 21287
Phone: 410-502-0468
Fax: 410-614-3676

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Re: [Freesurfer] edits to pial surface

[Dana W. Moore]

Hi Bruce,

Thanks for the suggestion.  Which function should I use to fix 
segmentation/topology errors?

Thanks,
Dana

At 10:24 AM 11/17/2009, Bruce Fischl wrote:
>Hi Dana,
>
>what's the bright stuff out near the pial surface? Is it dura? It's 
>hard to tell from just a single slice. If it is, then you could try 
>erasing it. Looks like there were also segmentation/topology fixing 
>errors in the right superior temporal gyrus, which you could fix. 
>Finally, you can try putting some control points near the base of 
>some off the wm strands in the left temporal white matter.
>
>cheers
>Bruce
>
>
>On Tue, 17 Nov 2009, Dana W. Moore wrote:
>
>>Hi everyone,
>>
>>I have an image in which the pial surface left out portions of the 
>>cortex (see left temporal lobe below).  I am not sure how to go 
>>about editing this. I tried adding control points to the 
>>brainmask.mgz volume and running -autorecon2-cp -autorecon3, but 
>>the result seems unchanged (see control points in picture 
>>below).  Did I do something wrong?  The edit voxels tool I believe 
>>would help if the problem was that these voxels had been removed 
>>during skull-stripping, but this is not the case--they were just 
>>excluded from the pial boundary.
>>
>>Thanks,
>>Dana
>>
>>Emacs!
>>
>>
>>
>>Dana W. Moore, Ph.D.
>>Neuropsychology Fellow
>>Cornell Neuropsychology Service
>>Weill Medical College of Cornell University
>>New York Presbyterian Hospital
>>Department of Neurology & Neuroscience
>>428 East 72nd Street, Suite 500
>>New York, NY 10021
>>Phone: 212-746-2823
>>Fax: 212-746-5584
>>Email: dwm2...@med.cornell.edu

Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2823
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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Re: [Freesurfer] Best way to convert Philips par/rec to mgz

[Douglas N Greve]

I think you can just run mri_convert, passing it one dicom file from the 
series, eg

mri_convert one.dcm 001.mgz

this will preserve the resolution.

doug

Julie McEntee wrote:
> Hello,
>
> I have T1-weighted data from Philips 3 T scanner obtained at a 
> resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec 
> (pixel size = int16) format. I would like to preserve the acquisition 
> resolution of the data in par/rec format; what is the best way to 
> convert such data to mgz format for analysis in freesurfer? A command 
> line example would be helpful, as I am new to freesurfer.
>
> Thanks for your help,
>
> Julie
>
> Julie E. McEntee, MA, CCRP
> Senior Research Program Coordinator
> Department of Psychiatry- Neuroimaging
> Johns Hopkins University School of Medicine
> 600 N. Wolfe St./Phipps 300
> Baltimore, MD 21287
> Phone: 410-502-0468
> Fax: 410-614-3676
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] edits to pial surface

[Bruce Fischl]

you'll need to either add control points and/or edit the wm.mgz
On Tue, 17 
Nov 2009, Dana W. Moore wrote:

> Hi Bruce,
>
> Thanks for the suggestion.  Which function should I use to fix 
> segmentation/topology errors?
>
> Thanks,
> Dana
>
> At 10:24 AM 11/17/2009, Bruce Fischl wrote:
>> Hi Dana,
>> 
>> what's the bright stuff out near the pial surface? Is it dura? It's hard to 
>> tell from just a single slice. If it is, then you could try erasing it. 
>> Looks like there were also segmentation/topology fixing errors in the right 
>> superior temporal gyrus, which you could fix. Finally, you can try putting 
>> some control points near the base of some off the wm strands in the left 
>> temporal white matter.
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Tue, 17 Nov 2009, Dana W. Moore wrote:
>> 
>>> Hi everyone,
>>> 
>>> I have an image in which the pial surface left out portions of the cortex 
>>> (see left temporal lobe below).  I am not sure how to go about editing 
>>> this. I tried adding control points to the brainmask.mgz volume and 
>>> running -autorecon2-cp -autorecon3, but the result seems unchanged (see 
>>> control points in picture below).  Did I do something wrong?  The edit 
>>> voxels tool I believe would help if the problem was that these voxels had 
>>> been removed during skull-stripping, but this is not the case--they were 
>>> just excluded from the pial boundary.
>>> 
>>> Thanks,
>>> Dana
>>> 
>>> Emacs!
>>> 
>>> 
>>> 
>>> Dana W. Moore, Ph.D.
>>> Neuropsychology Fellow
>>> Cornell Neuropsychology Service
>>> Weill Medical College of Cornell University
>>> New York Presbyterian Hospital
>>> Department of Neurology & Neuroscience
>>> 428 East 72nd Street, Suite 500
>>> New York, NY 10021
>>> Phone: 212-746-2823
>>> Fax: 212-746-5584
>>> Email: dwm2...@med.cornell.edu
>
> Dana W. Moore, Ph.D.
> Neuropsychology Fellow
> Cornell Neuropsychology Service
> Weill Medical College of Cornell University
> New York Presbyterian Hospital
> Department of Neurology & Neuroscience
> 428 East 72nd Street, Suite 500
> New York, NY 10021
> Phone: 212-746-2823
> Fax: 212-746-5584
> Email: dwm2...@med.cornell.edu
>
>
>
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[Freesurfer] recon - local directory

[Rajagopalan, Venkateswaran]

Dear Freesurfer users,
 
I don't have privileges to create directories in freesurfer installation folder 
as i am using freesurfer from server. So i am not able to run "recon-all -s 
Desktop/test/sub1/vol1.mgz -autorecon1" giving a path name to a folder in 
Desktop where my image volume is stored. So how to run this command.
 
Thanks in advance.
venkateswaran



===

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2009).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
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[Freesurfer] Qdec table

[Dankner, Nathan (NIH/NIMH) [F]]

Hi all,

I am attempting to create a qdec.table.dat file, and have been unable to find a 
way to paste my data into it in a way that will make it readable.  When I paste 
it in qdec always outputs an error when trying to open it, even if visually the 
file appears to be correct.  Is there an easy way to import data from excel 
into something readable by qdec?  I'm hoping to avoid having to manually enter 
everything because there is quite a lot of data, so any help would be 
appreciated.  Thanks,

Nathan

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Re: [Freesurfer] Qdec table

[Douglas N Greve]

If you're creating the file in windows, try running dos2unix on the file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:
> Hi all,
>
> I am attempting to create a qdec.table.dat file, and have been unable to find 
> a way to paste my data into it in a way that will make it readable.  When I 
> paste it in qdec always outputs an error when trying to open it, even if 
> visually the file appears to be correct.  Is there an easy way to import data 
> from excel into something readable by qdec?  I'm hoping to avoid having to 
> manually enter everything because there is quite a lot of data, so any help 
> would be appreciated.  Thanks,
>
> Nathan
>
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>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Qdec table

[Dankner, Nathan (NIH/NIMH) [F]]

Unfortunately I'm not running windows.  Are you familiar with any tricks I can 
use on a mac?


On 11/17/09 5:15 PM, "Douglas N Greve"  wrote:

If you're creating the file in windows, try running dos2unix on the file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:
> Hi all,
>
> I am attempting to create a qdec.table.dat file, and have been unable to find 
> a way to paste my data into it in a way that will make it readable.  When I 
> paste it in qdec always outputs an error when trying to open it, even if 
> visually the file appears to be correct.  Is there an easy way to import data 
> from excel into something readable by qdec?  I'm hoping to avoid having to 
> manually enter everything because there is quite a lot of data, so any help 
> would be appreciated.  Thanks,
>
> Nathan
>
> ___
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>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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Re: [Freesurfer] Qdec table

[Krish Subramaniam]

Some programs notoriously add Ctrl-M at the end of every line ( or  
every cell )

If you have the vi editor you can follow this method 
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/ 
  to remove all the instances of Ctrl-M and again try in qdec.  
Unfortunately I am not able to reproduce the error here because i  
don't have excel.

Here's another method : 
http://www.unix.com/shell-programming-scripting/25658-removing-control-ms-m.html

Best
Krish

On Nov 17, 2009, at 5:21 PM, Dankner, Nathan (NIH/NIMH) [F] wrote:

> Unfortunately I'm not running windows.  Are you familiar with any  
> tricks I can use on a mac?
>
>
> On 11/17/09 5:15 PM, "Douglas N Greve"   
> wrote:
>
> If you're creating the file in windows, try running dos2unix on the  
> file.
>
> doug
>
> Dankner, Nathan (NIH/NIMH) [F] wrote:
>> Hi all,
>>
>> I am attempting to create a qdec.table.dat file, and have been  
>> unable to find a way to paste my data into it in a way that will  
>> make it readable.  When I paste it in qdec always outputs an error  
>> when trying to open it, even if visually the file appears to be  
>> correct.  Is there an easy way to import data from excel into  
>> something readable by qdec?  I'm hoping to avoid having to manually  
>> enter everything because there is quite a lot of data, so any help  
>> would be appreciated.  Thanks,
>>
>> Nathan
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
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>
>

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Re: [Freesurfer] slopes of interaction analysis in tksurfer

[Douglas N Greve]

what do you mean by "see the slopes"? Those lines have a slope (it just 
looks like it is close to 0). Not sure why you can't see all 16, might 
be a limit in the fsgd visualization.

Stefan Brauns wrote:
> Hi all,
>
> I have done an analysis of thickness and a neuropsych variable as a 
> covariate with mri glmfit.
>
> I would now like to see the neuropsych slopes of different groups 
> (patients vs. controls) for certain vertices in tksurfer.
>
> After loading the sig.mgh overlay and the corresponding file 
> descriptor file, I can only view at the intercepts (see picture). Is 
> there a possibilty to show the slopes as well ?
>
> Furthermore the picture only shows 12 groups, although I have actually 
> 16 and I don't know why.
>
> Many thanks,
> Stefan
>
> -- 
> Stefan Brauns
> 15 Clark St
> Boston, MA, 02109
>
> phone: (617) 398-0437
> 
>
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] ICV for incomplete whole brain coverage

[Bruce Fischl]

that does look pretty good. My guess iss that the eTIV is also fine for 
this volume as it's only a 12 parameter transform, but I could be wrong 
(since I already was about our ability to accurately label this type of 
acquisition!)

Bruce
On Tue, 17 Nov 2009, Juranek, Jenifer wrote:

> Hi Bruce,
> I think you might underestimate the robustness of Freesurfer :)
> In case I'm being too picky, I've attached a couple of example screenshots.
>
> I appreciate that anyone rarely bothers with processing MRIs without whole 
> brain coverage, but I'm wondering if *anything* can be salvaged from this 
> dataset with many instances of incomplete brain coverage. I have 2 
> screenshots from the same subject (axial & sagittal planes) containing the 
> norm.mgz (**orig.mgz**) with the aseg.mgz overlay. This subject was processed 
> in FSv405. This example is not the worst (nor the best) example of incomplete 
> coveragevaries quite a bit across subjects. The aseg.mgz looks pretty 
> good. Will the ICV value generated by Freesurfer be accurate for correcting 
> subcortical aseg volumes by ICV? Are there any "rules of thumb" as to what is 
> necessary (in terms of brain/skull elements) for proper ICV values?
>
> Many Thanks for any comments,
> Jenifer
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, November 17, 2009 12:05 PM
> To: Juranek, Jenifer
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] ICV for incomplete whole brain coverage
>
> Hi Jenifer,
>
> how much is missing? If a substantial amount I would think things would
> fail, including the segmentation itself, but we very rarely do this.
>
> Bruce
>
>
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Re: [Freesurfer] slopes of interaction analysis in tksurfer

[Douglas N Greve]

Hard to say. Can you send me the fsgd file?

Stefan Brauns wrote:
> Thank you for your fast response.
>
> According to the vertex on the overlay map, there are differences in 
> the slopes of "red" and "blue" groups, that are not close to 0. One 
> can also see in the picture of the first mail, that the slopes of the 
> red groups should be definitely positive and at least some of all the 
> lines should cross each other.
>
> I would expect a picture like the one i have attached in this mail, 
> only with additional  "blue" lines in an opposite direction or close 
> to 0. in this picture, thereare also seperate lines for the mean 
> thickness of the groups and the slopes.
>
> Is it possible, that I have just to many groups and the fsgd 
> visualization can't show it correct?
>
> On Tue, Nov 17, 2009 at 6:33 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> what do you mean by "see the slopes"? Those lines have a slope (it
> just looks like it is close to 0). Not sure why you can't see all
> 16, might be a limit in the fsgd visualization.
>
> Stefan Brauns wrote:
>
> Hi all,
>
> I have done an analysis of thickness and a neuropsych variable
> as a covariate with mri glmfit.
>
> I would now like to see the neuropsych slopes of different
> groups (patients vs. controls) for certain vertices in tksurfer.
>
> After loading the sig.mgh overlay and the corresponding file
> descriptor file, I can only view at the intercepts (see
> picture). Is there a possibilty to show the slopes as well ?
>
> Furthermore the picture only shows 12 groups, although I have
> actually 16 and I don't know why.
>
> Many thanks,
> Stefan
>
> -- 
> Stefan Brauns
> 15 Clark St
> Boston, MA, 02109
>
> phone: (617) 398-0437
> 
> 
>
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>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
>
> -- 
> Stefan Brauns
> 15 Clark St
> Boston, MA, 02109
>
> phone: (617) 398-0437

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Qdec table

[Derin Cobia]

Nathan,

Here are the steps I use to create QDEC dat files on a Mac:

-Export/save your data in SPSS/Excel as a .csv file
-Open the .csv file in TextWrangler (a free text editor for Mac)
-Do a Find & Replace of the "," for " " to make it a space  
separated file
-Down at the bottom of the TextWrangler window is a drop down box to  
specify the type of hard returns ('Classic Mac' or 'Unix'); make sure  
the last line ends in a return

-Save as a ~.qdec.table.dat file

Hope that helps.

-Derin


On Nov 17, 2009, at 5:00 PM, Krish Subramaniam wrote:


Some programs notoriously add Ctrl-M at the end of every line ( or
every cell )

If you have the vi editor you can follow this method 
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/
 to remove all the instances of Ctrl-M and again try in qdec.
Unfortunately I am not able to reproduce the error here because i
don't have excel.

Here's another method : 
http://www.unix.com/shell-programming-scripting/25658-removing-control-ms-m.html

Best
Krish

On Nov 17, 2009, at 5:21 PM, Dankner, Nathan (NIH/NIMH) [F] wrote:


Unfortunately I'm not running windows.  Are you familiar with any
tricks I can use on a mac?


On 11/17/09 5:15 PM, "Douglas N Greve" 
wrote:

If you're creating the file in windows, try running dos2unix on the
file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:

Hi all,

I am attempting to create a qdec.table.dat file, and have been
unable to find a way to paste my data into it in a way that will
make it readable.  When I paste it in qdec always outputs an error
when trying to open it, even if visually the file appears to be
correct.  Is there an easy way to import data from excel into
something readable by qdec?  I'm hoping to avoid having to manually
enter everything because there is quite a lot of data, so any help
would be appreciated.  Thanks,

Nathan

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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